feat: add shell_run() and exec_in_context() + basic tests

pyproject.toml

@@ -34,8 +34,9 @@ classifiers = [
 requires-python = ">=3.10"
 dependencies = [
     "biopython",
-    "pandas",
     "Click >= 8.1.3",
+    "pandas",
+    "requests"
 ]
 
 [project.optional-dependencies]

src/ccbr_tools/util.py

@@ -0,0 +1,20 @@
+""" Miscellaneous utility functions """
+import contextlib
+import io
+import subprocess
+
+
+def shell_run(command_str):
+    """Run a shell command and return stdout/stderr"""
+    out = subprocess.run(command_str, capture_output=True, shell=True, text=True)
+    return "\n".join([out.stdout, out.stderr])
+
+
+def exec_in_context(func, *args, **kwargs):
+    """Execute a function in a context manager to capture stdout/stderr"""
+    with contextlib.redirect_stdout(io.StringIO()) as out_f, contextlib.redirect_stderr(
+        io.StringIO()
+    ) as err_f:
+        func(*args, **kwargs)
+        out_combined = "\n".join([out_f.getvalue(), err_f.getvalue()])
+    return out_combined

tests/test_cli.py

@@ -1,2 +1,7 @@
-def test_example():
-    assert True
+from ccbr_tools.util import shell_run
+
+
+def test_help_jobby():
+    assert "Will take your job(s)... and display their information!" in shell_run(
+        "jobby -h"
+    )

tests/test_util.py

@@ -0,0 +1,5 @@
+from ccbr_tools.util import exec_in_context
+
+
+def test_exec():
+    assert exec_in_context(print, "hello", "world") == "hello world\n\n"